tbuckley/cabot-search huggingface dataset:
Abstract 2929: High-Definition Digital PCR (HDPCR™) enables sensitive measurement of DNA and RNA variants in non-small cell lung cancer samples
Authors: Bryan Leatham, Katie McNall, Hari K. Subramanian, John Alvarado, Lucien Jacky, Mimi Wang, Aditya Rajagopal, Jerrod Schwartz
Journal: Cancer Research (2022)

Abstract Digital PCR (dPCR) is an emerging platform for detecting genomic variants in cancer genomes due to its high sensitivity and fast time to result compared to massively parallel sequencing. However, translational oncology applications often require the measurement of more biomarkers than there are color channels available on dPCR platforms. One approach to address this is to split a sample across many wells and profile a subset of variants in each well. For input-limited samples, however, this results in fewer molecules being profiled in each well, resulting in a reduction in sensitivity and fewer samples processed per instrument run. ChromaCode has developed a research use only (RUO) high-definition digital PCR assay, for multiplexed detection of 14 DNA variants and 15 RNA fusion variants relevant in non-small cell lung cancer (NSCLC) samples. The assay is constructed using both amplitude modulation and multi-channel resilient signal encoding methods. Amplitude modulation enables different variants to generate a signal at different intensity levels in single color channel, allowing for greater than n targets in n color channels. In contrast, resilient encoding generates a signal in more than one color channel to create a form of error detecting code. DNA and RNA samples were obtained using a combination of synthetic templates, cell line nucleic acids, and commercially available reference materials. Samples were run with the HDPCR NSCLC RUO assay on the Thermo Fisher Absolute Q digital PCR system, and data analysis was performed with custom analysis algorithms. The HDPCR NSCLC RUO assay demonstrated a limit of detection as low as 10 variant copies in a 10,000 haploid human genome copy DNA background. By employing HDPCR technology on digital PCR systems, it is possible to build a comprehensive and sensitive research assay that quickly detects many genomic alterations relevant to NSCLC samples. Citation Format: Bryan Leatham, Katie McNall, Hari K. Subramanian, John Alvarado, Lucien Jacky, Mimi Wang, Aditya Rajagopal, Jerrod Schwartz. High-Definition Digital PCR (HDPCR™) enables sensitive measurement of DNA and RNA variants in non-small cell lung cancer samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2929.
Abstract LB541: The cysteine rich protein 61 (Cyr61) contributes to tumor proliferation and invasion via HGF (hepatocyte growth factor) mediated NFkB signaling pathway in human hepatocellular carcinoma
Authors: Jiyoon Jung, sungae Koh, Kyunghee Lee, Jaeryong Kim
Journal: Cancer Research (2022)

Abstract Background: CCN growth factor family regulates a variety of biological events such as cell proliferation, cell invasion, cell differentiation, apoptosis, and growth inhibition. Cysteine-rich protein 61 (Cyr61) is one of six secreted proteins in the CCNs. It has been shown that Cyr61 plays an important role in tumorigenesis and carcinogenesis in glioma, breast cancer, and gastric cancer, and others. However, Cyr61 has not yet been elucidated on the tumorigenesis, proliferation, and invasion of hepatocellular carcinoma, and needs to be researched and discovered. In this study, the HGF-mediated association of Cyr61, interleukin-8 (IL-8), and NF-κB (Nuclear factor kappa-light-chain-enhancer of activated B cells) and cancer cell proliferation and invasion were investigated in two types of hepatoma cell lines. Methods: In this study, cell culture, cDNA microarray analysis, western blotting, Real-time Polymerase chain reaction, Zymography, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, Cyr61 knock-down with short hairpin RNA (shRNA), chromatin immunoprecipitation assay, Standard two chamber invasion assay. Results: First, we confirmed that the expression level of Cyr61 was up-regulated by HGF (hepatocyte growth factor) in hepatoma cells. To identify associated pathway of HGF-induced Cyr61 about IL-8, NF-κB expression, the cells were treated with PI3K (Phosphoinositide 3-kinase) inhibitor (LY294002) and then analyzed by Western blotting. The HGF-mediated IL-8 and NF-κB levels were decreased with LY294002. The role for Cyr61 associated with IL-8 and NF-κB was determined by knock down cell of Cyr61. Cyr61-sh RNA cells showed a decreased level of IL-8 and NF-κB. HGF-mediated cell proliferation and invasion were decreased in Cyr61 knock down cell. Conclusions: These results suggest that Cry61 plays an important role in cell proliferation and metastasis in hepatocellular carcinoma, and Cry61 may be a novel target for the prevention of progression and treatment of hepatocellular carcinoma. Citation Format: Jiyoon Jung, sungae Koh, Kyunghee Lee, Jaeryong Kim. The cysteine rich protein 61 (Cyr61) contributes to tumor proliferation and invasion via HGF (hepatocyte growth factor) mediated NFkB signaling pathway in human hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB541.
Abstract 4065: Efficacy of the Rac/Cdc42 inhibitor MBQ-167 in combination therapy with Paclitaxel
Authors: Ailed M. Cruz-Collazo, Olga Katsara, Elizabeth Salvo, Jean Ruiz, Robert Schneider, Suranganie Dharmawardhane
Journal: Cancer Research (2022)

Abstract Triple negative breast cancer (TNBC) represents a challenge because of its aggressiveness and resistance to standard chemotherapy. Since TNBC lacks targeted therapy options, the frontline therapy is Paclitaxel, which targets actively dividing cells inducing subsequent apoptosis. Since dormant cells or metastatic cancer cells are not targeted by Paclitaxel, more targeted treatment options are needed. MBQ-167, a small molecule developed by us to target the metastasis drivers Rac and Cdc42, is highly effective in reducing tumor growth and metastasis in mouse models of TNBC (Cruz-Collazo et al., 2021, Molecular Cancer Therapeutics). The purpose of this study is to test the hypothesis that MBQ-167 is a viable candidate for combined therapy with Paclitaxel in TNBC. Therefore, we tested the efficacy of MBQ-167 in combination with Paclitaxel in MDA-MB-231 human TNBC cells via MTT viability assays and caspase 3/7 apoptosis, using effective concentrations of MBQ-167 and/or Paclitaxel for 24, 48, 96 &amp; 120 hrs. We found that individual MBQ-167 or the combination therapy was more effective at 48-120 hrs at reducing cell viability by ~80% compared to ~60% by Paclitaxel treatment alone and significatively increasing apoptosis. Next, we tested individual or combined MBQ-167 (5 mg/kg 5X a week) and Paclitaxel (10 mg/kg 1X a week) on SCID mice bearing MDA-MB-231 tumors, via intraperitoneal administration. We report a significant reduction in tumor growth and lung metastasis in response to combined MBQ-167 and Paclitaxel compared to either treatment alone. A more aggressive syngeneic model of 4T-1 mouse breast cancer cells in BALB/c immunocompetent model was used to determine the direct effect of MBQ-167 and Paclitaxel on metastasis. When 4T-1 tumors were surgically removed and MBQ-167, Paclitaxel, or the combination administered for 17 days, the combination treatment, but not individual compounds, significantly reduced lung metastases by ~80%. In conclusion, this study validates the clinical testing of MBQ-167 in combination with Paclitaxel as a potential therapeutic for TNBC. Citation Format: Ailed M. Cruz-Collazo, Olga Katsara, Elizabeth Salvo, Jean Ruiz, Robert Schneider, Suranganie Dharmawardhane. Efficacy of the Rac/Cdc42 inhibitor MBQ-167 in combination therapy with Paclitaxel [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4065.
Abstract 217: A novel class of dimeric quinacrine compounds induce DNA damage and increase the anticancer activity of radiation
Authors: Ilias V. Karagounis, Jayashree Karar, Christoforos Thomas, Constantinos Koumenis, Jeffrey Winkler, Ravi Amaravadi, Amit Maity
Journal: Cancer Research (2022)

Abstract Radiation therapy is commonly used to treat cancers in the definitive setting, but the local control often remains suboptimal, thereby motivating us to search for novel radiosensitizers. Recently a series of novel quinacrines based upon a previously reported dimeric chloroquine has been synthesized. We studied one of these agents, DQ660. By itself, the drug upregulates both p53 protein and p53 transcriptional targets and also increases apoptosis in p53-wildtype H460 lung cancer cells. Furthermore, we found that DQ660 is a potent radiosensitizer in vitro. This radiosensitization is not contingent upon wildtype p53 as it occurs in cells null for p53 and containing mutant p53. The combination of radiation and DQ660 proded significant growth retardation of human xenografts grown in vivo compared to radiation or DQ660 alone. We saw higher levels of γ-H2AX foci with combined treatment compared to either alone, suggesting that the drug increases DNA damage induction. Using agarose gel electrophoresis and kinetoplast DNA (kDNA) as a substrate, we found that DQ660 can inhibit topoisomerase II activity. DQ660 did not potentiate the phosphorylation of ATM at S1981 seen after radiation. However, the drug did lead to an increase in Ser428 phosphorylation of ATR. This phosphorylation was not seen in response to radiation alone, suggesting that DQ660 and radiation activate different signaling pathways in response to DNA damage. We saw similar results with another dimeric quinacrine, DQ550, suggesting that this class of agents may be radiosensitizers. Our findings have uncovered a novel class of radiosensitizers that work at nanomolar concentrations and will spur investigations for its use in combination therapy for tumors treated with radiation Citation Format: Ilias V. Karagounis, Jayashree Karar, Christoforos Thomas, Constantinos Koumenis, Jeffrey Winkler, Ravi Amaravadi, Amit Maity. A novel class of dimeric quinacrine compounds induce DNA damage and increase the anticancer activity of radiation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 217.
Abstract 674: Tracking the transcriptome of lung cancer-associated fibroblasts within the TRACERx lung study from patient to culture models reveals phenotypic plasticity and instructive cues from cancer cells
Authors: Yutaka Naito, Robert Hynds, David Novo, Probir Chakravarty, Gavin Kelly, Charles Swanton, Kazufumi Honda, Erik Sahai
Journal: Cancer Research (2022)

Abstract Cancer-associated fibroblasts (CAFs) play a pivotal role in cancer progression by enhancing extracellular matrix remodeling, cancer cell invasion, and mediating inflammatory environment. Therefore, CAFs have become targets for cancer therapies. However, a major hurdle to developing such therapies are the challenges of studying CAFs in culture - specifically it remains unclear which CAF functions and phenotypes are sustained during in vitro culture and the signaling pathways driving distinct CAF phenotypes. We investigated whether CAF phenotypes and functions are sustained or changed during 2D CAF culture under in vitro systems, our analysis included early passage, late passage, and immortalized cultures, as well as CAFs in coculture with cancer cell lines. Transcriptomic analysis revealed that inflammatory-related gene expression programs were suppressed in late passage and immortalized CAFs compared with early passage equivalents. Direct co-culture with lung cancer cells can revert the inflammatory gene expressions in immortalized CAFs such that they partially resemble early passage CAFs. In contrast, indirect coculture with lung cancer cells - in which CAFs could not form cell-cell contacts with cancer cells - had a less significant effect on immortalized CAF inflammatory gene expression but could induce TGFβ regulated genes. Interestingly, inhibition of the TGFβ signaling pathway potentiated the inflammatory gene expression network induced by direct co-culture, suggesting that the signaling mediated by direct cellular interaction is antagonistic to the TGFβ signaling pathway. These data further our understanding of cancer cell – CAF crosstalk and will help to develop in vitro assays that more closely maintain the state of CAFs observed in tissue. Citation Format: Yutaka Naito, Robert Hynds, David Novo, Probir Chakravarty, Gavin Kelly, Charles Swanton, Kazufumi Honda, Erik Sahai, TRACERx Consortium. Tracking the transcriptome of lung cancer-associated fibroblasts within the TRACERx lung study from patient to culture models reveals phenotypic plasticity and instructive cues from cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 674.
Abstract 5381: Combinatory effect of EZH2 inhibitor and dopamine D1 receptor agonist enhance inhibition of triple negative breast cancer cell growth
Authors: Prem Prakash Kushwaha, Shiv Verma, Gautham Sarathy, Anmol Kumar, Sanjay Gupta, Bhuvaneswari Ramaswamy, Sarmila Majumder, Eswar Shankar
Journal: Cancer Research (2022)

Abstract Treatment for Triple Negative Breast Cancer remains a challenge due to its aggressive behavior; poor clinical outcome and disposition to therapeutic resistance. The diverse clinical and molecular characteristics drives high level of heterogeneity in breast cancer. Overall change in the epigenome triggers oncogenic activity of enhancer of zeste homolog 2 (EZH2) causing changes in gene expression that leads to cancer progression. EZH2 is the catalytic member of the Polycomb group protein complex that provides the active site for covalent methylation reactions. High expression of EZH2 is strongly associated with aggressive TNBC phenotypes, compared to other non-TNBCs. Development of resistance to EZH2 inhibitors limit their therapeutic use. Studies have shown that dopamine receptor (DR) agonists and antagonists alter TNBC cell growth in both in vitro and in vivo models. Our objective was to investigate if a combination of a D1R agonist with an EZH2 inhibitor was effective to attenuate TNBC cell proliferation. Docking studies were performed using Schrodinger software and visualization software to determine the affinity of GSK126 and SKF38393 towards EZH2. TNBC cells were treated individually and combined with EZH2 inhibitor, GSK126, and D1 agonist SKF38393 for cell viability and immunoprecipitation. Insilco analysis using docking studies revealed that SKF38393 actively interacts in the same region where GSK126 binds to EZH2 i.e. the catalytic site. Combination treatment of TNBC cells with GSK126 and SKF38393 caused synergistic inhibition of cell viability, suppressed the H3K27 trimethylation activity, and inhibited invasion of TNBC cells. Immunoprecipitation of EZH2 in the presence of GSK126 and SKF38393 dissociated the association between EZH2, EED, and SUZ12 in MDA-MB-231 cells. We report that combination of GSK126 and SKF38393 may have an enhanced efficacy in inhibiting the catalytic function of EZH2. The combined treatment of TNBC cells with GSK126 and SKF38393 inhibit TNBC proliferation by disrupting EZH2 functions. (This work is supported by DOD: W81XWH2010065, for Eswar Shankar) Citation Format: Prem Prakash Kushwaha, Shiv Verma, Gautham Sarathy, Anmol Kumar, Sanjay Gupta, Bhuvaneswari Ramaswamy, Sarmila Majumder, Eswar Shankar. Combinatory effect of EZH2 inhibitor and dopamine D1 receptor agonist enhance inhibition of triple negative breast cancer cell growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5381.
In the phase III IMmotion151 trial of metastatic renal cell carcinoma the easy-to-implement modified Glasgow prognostic score predicts outcome more accurately than the IMDC score
Authors: J. Saal, T. Bald, M. Hölzel, M. Ritter, P. Brossart, J. Ellinger, N. Klümper
Journal: Annals of Oncology (2022)
Abstract 1466: MYC localizes to the nuclear pore to promote DNA repair during replication stress
Authors: Gabriel Cohn, Colin J. Daniel, Daniel F. Liefwalker, Rosalie C. Sears
Journal: Cancer Research (2022)

Abstract Genomic instability is a hallmark of cancer which promotes oncogenic mutations in pancreatic ductal adenocarcinoma (PDAC), leading to more aggressive tumors with greater potential for drug resistance. Deregulation of the master transcription factor, MYC, is found in virtually all PDAC tumors and promotes genomic alterations by increasing replication stress, augmenting DNA repair pathways, and promoting cell survival. To resolve replication stress, stalled forks are trafficked to the nuclear pores where the necessary machinery accumulates. Activated MYC is spatially reorganized to the nuclear pores as well, a mechanism that is exacerbated in cancer. Whether MYC activity at the nuclear pores contributes to resolving replication stress in PDAC remains to be known. To investigate this mechanism, we are creating genomic and proteomic tools to determine MYC’s function at the nuclear pores during replication stress induced by olaparib treatment in PDAC cells. We found that olaparib significantly increases MYC accumulation at the nuclear pore in low-passage cell lines we established from PDAC patient tumors. Furthermore, we showed that MYC interacts with the nuclear pore resident SUMO protease, SENP1, which plays a key role in resolving stalled forks. Our preliminary data suggest a role for MYC resolving replication stress at nuclear pores, and could indicate MYC activity as a therapeutic target in olaparib-resistant PDAC. Citation Format: Gabriel Cohn, Colin J. Daniel, Daniel F. Liefwalker, Rosalie C. Sears. MYC localizes to the nuclear pore to promote DNA repair during replication stress [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1466.
Abstract 2448: Mmp-2 facilitates prostate cancer entry into and exit from dormancy
Authors: Mostafa Nasr
Journal: Cancer Research (2022)

Abstract Prostate cancer (PC) patients often relapse with skeletal metastases years after remission. This is attributed to the dormancy program acquired by disseminated tumor cells (DTCs) in the bone microenvironment. Understanding the molecular mechanisms driving dormancy &amp; reawakening (D&amp;R) can reveal novel therapeutic opportunities. Matrix metalloproteinases (MMPs) are involved in each step of the metastatic cascade. Recent studies have shown upregulation of MMP-2 expression in D&amp;R. To determine whether MMP-2 plays a causal role, we initially developed a model representing dormancy in PC cell lines using basal growth conditions and high seeding density. The generated dormant cells (D-Cs) formed clusters and had negative expression of Ki-67 (98% of cells, p = 0.007), Low ERK/P38 activity ratio (p = 0.002), and higher percentage of G0/G1 arrested cells (p = 0.0004). The clusters can remain dormant and viable even after long-term culture (&amp;gt;28 days). We observed that D-Cs can reawaken in-vitro by re-introducing serum-containing media. Next, we assessed MMP-2 expression in D-Cs and reawakened cells. We found MMP-2 expressed during entry into dormancy but highly upregulated during reawakening. Using a siRNA approach, we found that MMP-2 silencing prevented entry into dormancy by significantly inhibiting cluster formation and survival. To determine the role of MMP-2 in reawakening, we used a pharmacological approach due to the temporal nature of MMP-2 silencing by siRNA. Using a highly selective bisphosphonate-based MMP-2 inhibitor (ML115), we found that blocking MMP-2 activity prevented the reawakening of prostate cancer cells without impacting cell viability at 1µM as assessed by caspase-3 cleavage via immunoblotting. In conclusion, we developed an in-vitro PC-specific model for dormancy &amp; reawakening. We found MMP-2 to be key for controlling entry and exit from dormancy in-vitro. We are currently elucidating the mechanisms through which MMP-2 mediates these effects. We also posit that our selective bone-targeting MMP-2 inhibitor may be effective in blocking the reawakening of dormant cells in-vivo. Citation Format: Mostafa Nasr. Mmp-2 facilitates prostate cancer entry into and exit from dormancy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2448.
Abstract 5109: Development of cfDNA reference standards for methylation-sequencing tests
Authors: Bingsi Li, Jing Su, Jiayue Xu, Guangliang Zhang, Xiaoling Li, Ya Zhou, Hao Wang, Shuai Fang, Zhihong Zhang
Journal: Cancer Research (2022)

Abstract Introduction: Recently, methylation sequencing has drawn significant attention as it has shown great promise for cancer detection and relapse surveillance. However, as with any low-input sequencing method, quality control is critical for implementation into the clinic, and it is difficult to obtain a sustainable source of patient samples for validation activities. To address these unmet needs, here we describe a design of fit-for-purpose cfDNA Methylation Reference Standards (MRS) to evaluate the performance of cfDNA-based methylation tests for oncology. Methods: We analyzed the genome-wide methylation landscape of 6 human cancer cell lines, 4 normal human lymphocyte cell lines, and 24 healthy donor cfDNA samples via whole genome bisulfite sequencing (WGBS), the gold standard of methylation analysis. Using cancer cell line genomic DNA cleaved by double-stranded DNA endonuclease (Zymo), we developed a range of cfDNA MRS spanning clinically relevant tumor fractions. DNA fragmentation were validated using the Labchip system (Perkin Elmer) and tumor fractions were independently verified by droplet digital PCR (Biorad). Results: The MRS series represent surrogates for lung, colorectal, liver, ovarian, pancreatic, and esophageal cancers. They display a size distribution comparable to cfDNA extracted from plasma, and represent a broad range of tumor fractions from 10% to 0.01%. In addition, the assembly accuracy was confirmed by digital droplet PCR (ddPCR) and ultra-deep mutation sequencing. Conclusions: These results demonstrated that the analytical feature and clinical relevance of MRS provides a versatile tool for assay optimization, validation, and cross-platform comparison. Citation Format: Bingsi Li, Jing Su, Jiayue Xu, Guangliang Zhang, Xiaoling Li, Ya Zhou, Hao Wang, Shuai Fang, Zhihong Zhang. Development of cfDNA reference standards for methylation-sequencing tests [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5109.